Characterization of Neisseria meningitidis isolates collected from 1974 to 2003 in Japan by multilocus sequence typing

2004 ◽  
Vol 53 (7) ◽  
pp. 657-662 ◽  
Author(s):  
Hideyuki Takahashi ◽  
Toshiro Kuroki ◽  
Yuko Watanabe ◽  
Hiroshi Tanaka ◽  
Hiroo Inouye ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Neisseria Meningitidis ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
The Other ◽  
Mlst Database ◽  
Mlst Analysis ◽  
The Past ◽  
Sequence Types

Analysis of 182 Neisseria meningitidis strains isolated over the past 30 years in Japan by serogroup typing and multilocus sequence typing (MLST) was performed. The serogroups of the 182 Japanese isolates were B (103 isolates), Y (39), W135 (1) and non-groupable (39). By MLST analysis, 65 different sequence types (ST) were identified, 42 of which were not found in the MLST database as of January 2004 and seemed to be unique to Japan. Statistical analysis of the MLST results revealed that, although the Japanese isolates seemed to be genetically divergent, they were classified into six major clonal complexes and other minor complexes. Among these isolates, well-documented ST complexes found worldwide were present, such as ST-23 complex (49 isolates), ST-44 complex (41 isolates) and ST-32 complex (8 isolates). On the other hand, a new clonal complex designated ST-2046 complex (28 isolates), which has not been identified in other countries, was also found, suggesting that this clone was indigenous to Japan. Taken together, it was speculated that meningococcal isolates in Japan comprised heterogeneous clones, which were derived both from clones identified in other countries and clones unique to Japan.

scholarly journals Characterization of Streptococcus pneumoniae isolates from India with special reference to their sequence types

2013 ◽  
Vol 7 (02) ◽  
pp. 101-109 ◽  
Author(s):  
Malini Shariff ◽  
Jyoti Choudhary ◽  
Shazia Zahoor ◽  
Monorama Deb
Keyword(s):  
Streptococcus Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
The Elderly ◽  
New Delhi ◽  
Broth Microdilution ◽  
Mortality And Morbidity ◽  
Resistance To Penicillin ◽  
Sequence Types

Introduction: Streptococcus pneumoniae is a major cause of mortality and morbidity in young children and the elderly. In the present study we evaluated antimicrobial susceptibilities, serotypes, and sequence types of pneumococcal isolates recovered in New Delhi, India. Methodology: A total of 126 clinical isolates of Streptococcus pneumoniae were investigated. They were subjected to disk diffusion susceptibility testing, broth microdilution testing, serotyping and multilocus sequence typing. Results: Broth microdilution assay showed that 5%, 20% and 23% of the isolates exhibited resistance to penicillin, erythromycin and ciprofloxacin, respectively. Serotypes19, 1 and 6 were more frequently isolated. Thirty per cent of the strains were comprised of serotypes 1, 3, 5, 19A and 7F, which are not included in the seven-valent vaccine. Fifty-nine isolates were typed using multilocus sequence typing. Thirty new sequence types were encountered in this study. Only one clonal complex with 4 isolates was seen; 11 clonal complexes and 96 sequence types (STs) were observed among 115 Indian isolates. Only 18 of the 96 STs were found globally, of which only 4 STs were found in many countries with larger numbers. Conclusions: This study identifies the non-vaccine serotypes of Streptococcus pneumoniae circulating in India. It is important that an appropriate vaccine which covers all serotypes is used in the region.

scholarly journals Clonal analysis of the serogroup B meningococci causing New Zealand's epidemic

2005 ◽  
Vol 134 (2) ◽  
pp. 377-383 ◽  
Author(s):  
K. H. DYET ◽  
D. R. MARTIN
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
16S Rrna ◽  
Meningococcal Disease ◽  
Common Ancestor ◽  
Clonal Complex ◽  
Clonal Analysis ◽  
The Other ◽  
Disease Rates ◽  
Sequence Types

An epidemic of meningococcal disease caused by serogroup B meningococci expressing the P1.7-2,4 PorA protein began in New Zealand in 1991. The PorA type has remained stable. Different porB have been found in association with the P1.7-2,4 PorA, although type 4 has been most common. The clonal origins of B:P1.7-2,4 meningococci isolated from cases during 1990 to the end of 2003 were analysed. In 1990, the year immediately preceding the recognized increase in disease rates, all three subclones (ST-41, ST-42, and ST-154) of the ST-41/44 clonal complex occurred among the five isolates of B:P1.7-2,4. The two sequence types, ST-42 and ST-154, continued to cause most disease throughout New Zealand. Isolates belonging to subclone ST-41 were mostly identified early in the epidemic and in the South Island. 16S rRNA typing indicated that isolates belonging to the subclones ST-41 and ST-154 share a common ancestor, with those typing as ST-42 more distantly related with some genetically ambiguous. It is possible that ST-41 and ST-154 may have evolved one from the other but evolution to ST-42 is more difficult to explain. It is possible that one or more of the ST types could have been introduced into New Zealand prior to the first detection of clinical cases in 1990. Genetic diversity may have occurred during carriage in the community.

Statistics and Economic History

1941 ◽  
Vol 1 (1) ◽  
pp. 26-41 ◽  
Author(s):  
Simon Kuznets
Keyword(s):  
Statistical Analysis ◽  
Economic History ◽  
Raw Materials ◽  
The Other ◽  
Economic Study ◽  
Statistical Research ◽  
Historical Approach ◽  
The Past ◽  
Economic Inquiry ◽  
Analytical Tools

This paper deals with the relation between statistical analysis as applied in economic inquiry and history as written or interpreted by economic historians. Although both these branches of economic study derive from the same body of raw materials of inquiry—the recordable past and present of economic society—each has developed in comparative isolation from the other. Statistical economists have failed to utilize adequately the contributions that economic historians have made to our knowledge of the past; and historians have rarely employed either the analytical tools or the basic theoretical hypotheses of statistical research. It is the thesis of this essay that such failure to effect a close interrelation between historical approach and statistical analysis needs to be corrected in the light of the final goal of economic study.

scholarly journals Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2035-2045 ◽  
Author(s):  
Claudia Picozzi ◽  
Gaia Bonacina ◽  
Ileana Vigentini ◽  
Roberto Foschino
Keyword(s):  
Multilocus Sequence Typing ◽  
Geographical Area ◽  
Housekeeping Genes ◽  
Processing Conditions ◽  
Clonal Population ◽  
Factors Affecting ◽  
Lactobacillus Sanfranciscensis ◽  
Mlst Scheme ◽  
Sequence Types

Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.

scholarly journals rhs Genes Are Potential Markers for Multilocus Sequence Typing of Escherichia coli O157:H7 Strains

2009 ◽  
Vol 75 (18) ◽  
pp. 5853-5862 ◽  
Author(s):  
K. Liu ◽  
S. J. Knabel ◽  
E. G. Dudley
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Multilocus Sequence Typing ◽  
Sequence Variation ◽  
Escherichia Coli O157 ◽  
Positive Selection Pressure ◽  
E Coli ◽  
The Past ◽  
Unique Markers ◽  
Sequence Types

ABSTRACT DNA sequence-based molecular subtyping methods such as multilocus sequence typing (MLST) are commonly used to generate phylogenetic inferences for monomorphic pathogens. The development of an effective MLST scheme for subtyping Escherichia coli O157:H7 has been hindered in the past due to the lack of sequence variation found within analyzed housekeeping and virulence genes. A recent study suggested that rhs genes are under strong positive selection pressure, and therefore in this study we analyzed these genes within a diverse collection of E. coli O157:H7 strains for sequence variability. Eighteen O157:H7 strains from lineages I and II and 15 O157:H7 strains from eight clades were included. Examination of these rhs genes revealed 44 polymorphic loci (PL) and 10 sequence types (STs) among the 18 lineage strains and 280 PL and 12 STs among the 15 clade strains. Phylogenetic analysis using rhs genes generally grouped strains according to their known lineage and clade classifications. These findings also suggested that O157:H7 strains from clades 6 and 8 fall into lineage I/II and that strains of clades 1, 2, 3, and 4 fall into lineage I. Additionally, unique markers were found in rhsA and rhsJ that might be used to define clade 8 and clade 6. Therefore, rhs genes may be useful markers for phylogenetic analysis of E. coli O157:H7.

A Stylometric Analysis of Iranian Poets

2017 ◽  
Vol 7 (1) ◽  
pp. 55 ◽  
Author(s):  
Sohrab Rezaei ◽  
Nasim Kashanian
Keyword(s):  
Statistical Analysis ◽  
Computer Program ◽  
Word Length ◽  
The Other ◽  
The Past ◽  
Authorship Analysis

This paper presents an investigation into the extent to which the lexical choices made by different poets are distinctive. When a writer, writes, s/he makes lexical choices that make them different from other writers and the writing to some extent can be considered as their fingerprint or in the other word their signature. Authorship analysis by means of textual measurements has been the interest of so many linguists. Authors have their own styles and the stylometrist is interested in finding units which can distinct authors from each other. Statistical analysis has provided different tools for this attempt, by different scholars. Over the past 3 centuries many types of textual tools has been introduced to discriminate different authors objectively that developing in computer programing has played the important role for using these models. In this study by writing a computer program, the styles of different Iranian poets, Attar and Molavi, and Nezami, are investigated in terms of their word length and word richness. Result shows differences between their styles in terms of these parameters. This way of analyzing writing of different authors has some implications in different field of sociolinguistic and TOEFL.

scholarly journals First Insights into the Evolution of Streptococcus uberis: a Multilocus Sequence Typing Scheme That Enables Investigation of Its Population Biology

2006 ◽  
Vol 72 (2) ◽  
pp. 1420-1428 ◽  
Author(s):  
Tracey J. Coffey ◽  
Gillian D. Pullinger ◽  
Rachel Urwin ◽  
Keith A. Jolley ◽  
Stephen M. Wilson ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Bovine Mastitis ◽  
Housekeeping Gene ◽  
Global Scale ◽  
Streptococcus Uberis ◽  
Capsule Production ◽  
Sequence Types ◽  
Better Than

ABSTRACT Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis throughout the world. Several procedures to differentiate S. uberis isolates have been proposed. However, all are prone to interlaboratory variation, and none is suitable for the description of the population structure. We describe here the development of a multilocus sequence typing (MLST) scheme for S. uberis to help address these issues. The sequences of seven housekeeping gene fragments from each of 160 United Kingdom milk isolates of S. uberis were determined. Between 5 and 17 alleles were obtained per locus, giving the potential to discriminate between 1.3 × 107 sequence types. In this study, 57 sequence types (STs) were identified. Statistical comparisons between the maximum-likelihood trees constructed by using the seven housekeeping gene fragments showed that the congruence was no better than that between each tree and trees of random topology, indicating there had been significant recombination within these loci. The population contained one major lineage (designated the ST-5 complex). This dominated the population, containing 24 STs and representing 112 isolates. The other 33 STs were not assigned to any clonal complex. All of the isolates in the ST-5 lineage carried hasA, a gene that is essential for capsule production. There was no clear association between ST or clonal complex and disease. The S. uberis MLST system offers researchers a valuable tool that allows further investigation of the population biology of this organism and insights into the epidemiology of this disease on a global scale.

scholarly journals Molecular characterization of serogroup C Neisseria meningitidis isolated in China

2007 ◽  
Vol 56 (9) ◽  
pp. 1224-1229 ◽  
Author(s):  
Xiaobing Zhang ◽  
Zhujun Shao ◽  
E Yang ◽  
Li Xu ◽  
Xingye Xu ◽  
...  
Keyword(s):  
Bacterial Meningitis ◽  
Neisseria Meningitidis ◽  
Variable Region ◽  
Molecular Characteristics ◽  
Virulent Strains ◽  
Sporadic Cases ◽  
High Level ◽  
Sequence Types ◽  
Close Contacts

An increase in the number of serogroup C meningococcal disease cases occurred in China from September 2003 to January 2006 as a result of several successive outbreaks. In addition, the proportion of serogroup C Neisseria meningitidis isolates from sporadic cases and carriers has also increased. In this study, 113 serogroup C meningococcal isolates were characterized by multilocus sequence typing (MLST) and PorA typing. These isolates comprised those from outbreak cases and their close contacts, the national carriage survey conducted during the same period and some historical isolates from 1966–2002. Twenty MLST sequence types (STs) and 21 PorA variable region (VR) types were identified in the collection. The ST-4821 complex, a newly identified lineage, was the most prevalent lineage (95/113). These data also showed a high level of diversification of serogroup C isolates, as indicated by the number of variants of the ST-4821 clone and the VR types present. There were ten PorA VR types among the ST-4821 isolates, and certain VR types (P1.7-2,14, P1.12-1,16-8) were associated with isolates from outbreak cases. The results of this study allow us to draw a profile of the molecular characteristics of serogroup C strains in China. These data are helpful for monitoring the spread of virulent strains and will provide valuable information for the prevention of bacterial meningitis in China.

scholarly journals Determination of serotyping antigens, clonal analysis and genetic characterization of the 4CMenB vaccine antigen genes in invasive Neisseria meningitidis from Western Canada, 2009 to 2013

2014 ◽  
Vol 63 (11) ◽  
pp. 1490-1499 ◽  
Author(s):  
Dennis K. S. Law ◽  
Jianwei Zhou ◽  
Saul Deng ◽  
Linda Hoang ◽  
Gregory Tyrrell ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Clonal Complex ◽  
Factor H ◽  
Vaccine Antigen ◽  
Western Canada ◽  
Antigenic Analysis ◽  
Clonal Nature ◽  
4Cmenb Vaccine

This study examined invasive Neisseria meningitidis recovered from invasive meningococcal disease (IMD) cases in Western Canada between 2009 and 2013. A total of 161 isolates from individual IMD cases were analysed for serogroup, serotype, serosubtype, PorA genotype, multi-locus sequence type and nucleotide sequence of their 4CMenB vaccine antigen genes. Sixty-nine isolates were serogroup B (MenB), 47 were serogroup Y (MenY), 22 were serogroup C (MenC), 19 were serogroup W (MenW), three were serogroup E and one was non-encapsulated. MenC, MenY and MenW were mainly clonal, represented primarily by clonal complex (cc) 11, cc23 or cc167, and cc22, respectively. In contrast, MenB were composed of eight different ccs together with 11 isolates not assigned to any known cc. Antigenic analysis and PorA genotyping confirmed the heterogeneity of MenB isolates, while such results supported the clonal nature of most MenC, MenY and MenW isolates. Thirty-four (21.1 %) isolates had at least one gene that encoded one matching vaccine protein component of the 4CMenB vaccine (i.e. PorA P1.4; fHbp variant 1.1; NHBA peptide 2; and NadA-1, -2, or -3). An additional 18 isolates had genes that encoded variant 1 or subfamily B factor H binding proteins of this same vaccine.

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